The last six rows provide the percentage of the former families where MowgliNNI provides modified gene trees (resp. reconciliations) that are closer, equally far or farther from the true gene trees (resp. the true evolutions).
In addition to reductions in number of events and hence reconciliation cost, the modified gene trees proposed by MowgliNNI usually reduced the number of alternative MPRs, i.e. equally most parsimonious histories.
Then, a network displaying all clades present in at least one among the modified gene trees was computed using the Cass algorithm [ 57] implemented in Dendroscope 2 [ 58], inputted with the Z-closure of the modified trees [ 59].
The last six rows provide the percentage of the former families where MowgliNNI provides modified gene trees (resp. reconciliations) that are closer, equally far or farther from the true gene trees (resp. the true reconciliations).
Similar results were observed for the quality of modified gene trees(G NNI ) in term of RF distance to G True and for the quality of reconciliations in term of event distance between inferred and true reconciliation.
On a random sample of two dozens modified gene trees, the number of MPRs is reduced in 63% of the cases (by a factor of 18 in the best case), and increased in 21% (by a factor 3 at worst).
